Module Category Description
R lang R is a free software environment for statistical computing and graphics.
abinit chem ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
abseil lib Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
afni bio AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data. It is freely available (both in source code and in precompiled binaries) for research purposes. The software is made to run on virtually an Unix system with X11 and Motif displays. Binary Packages are provided for MacOS and Linux systems including Fedora, Ubuntu (including Ubuntu under the Windows Subsytem for Linux)
agrep tools AGREP - an approximate GREP.
alamode chem ALAMODE is designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the anharmonic force constants, you can also calculate lattice thermal conductivity from first principles.
alphafold bio Open source code for AlphaFold
alphapulldown bio AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer
amber chem Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
amptorch chem AMPtorch is a PyTorch implementation of the Atomistic Machine-learning Package (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers. AMPtorch is built on top of PyTorch Geometric and Skorch.
anaconda lang Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
angsd bio Program for analysing NGS data.
ansys cae ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
ant devel Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
ants data ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
anvio data Anvi'o is an open-source, community-driven analysis and visualization platform for microbial 'omics. It brings together many aspects of today's cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
aocc compiler AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM
apptainer tools Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems.
archspec tools A library for detecting, labeling, and reasoning about microarchitectures
aria2 tools aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
armadillo numlib Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
arpack-ng numlib ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
ase chem The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
aspera-connect tools Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
at-spi2-atk vis AT-SPI 2 toolkit bridge
at-spi2-core vis Assistive Technology Service Provider Interface.
atat chem The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools
atk vis ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
attrdict3 lib AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
augustus bio AUGUSTUS is a program to find genes and their structures in one or more genomes.
awscli tools This package provides a unified command line interface to Amazon Web Services.
axel tools Lightweight CLI download accelerator
bamtools bio BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
bart bio BART (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors (TFs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, given a query gene set or a ChIP-seq dataset as input.
bart-mri bio The Berkeley Advanced Reconstruction Toolbox (BART) toolbox is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging developed by the research groups of Martin Uecker (Goettingen University), Jon Tamir (UT Austin), and Michael Lustig (UC Berkeley). It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sen.
bazel devel Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.
bbmap bio BBMap includes a short read aligner, and other bioinformatic tools.
bcftools bio SAMtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
bcl2fastq2 bio bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
beagle bio Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.
bedops bio BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
bedtools bio The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
berkeley_db tools Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
bicseq2-norm bio BICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-seg bio BICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm.
binutils tools binutils: GNU binary utilities
bioawk bio Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.
bioconda bio Bioconda is a channel for the conda package manager specializing in bioinformatics software.
bioperl bio Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
biopython bio Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
bismark bio A tool to map bisulfite converted sequence reads and determine cytosine methylation states
bison lang Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
blasr bio Variation graphs provide a succinct encoding of the sequences of many genomes.
blast bio Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
blat bio BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
blender vis Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
blitz++ lib Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
boost devel Boost provides free peer-reviewed portable C++ source libraries.
bowtie2 bio Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
bsmap bio BSMAP is a short reads mapping program for bisulfite sequencing in DNA methylation study. Bisulfite treatment coupled with next generation sequencing could estimate the methylation ratio of every single Cytosine location in the genome by mapping high throughput bisulfite reads to the reference sequences.
bwa bio Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
bzip2 tools bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
cairo vis Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
canu bio Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
caviar bio caviar is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.
cc3d vis CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D's intuitive interface makes Virtual Tissue modeling accessible to users without extensive software development or programming experience.
cd-hit bio CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cellassign bio cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.
cellpose bio a generalist algorithm for cellular segmentation
cellprofiler bio CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
cellranger bio A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
cellranger-arc bio Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.
cellranger-atac bio Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
cellranger-dna bio Cell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.
cereal lib cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
cesm geo CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
cfitsio lib CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
cgal numlib The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
chemps2 chem CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
ciftilib lib C++ Library for reading and writing CIFTI-2 and CIFTI-1 files
circos bio Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
clang compiler C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.
clapack math C version of LAPACK
clara-parabricks bio NVIDIA Parabricks is the only GPU-accelerated computational genomics toolkit that delivers fast and accurate analysis for sequencing centers, clinical teams, genomics researchers, and next-generation sequencing instrument developers.
clearcut bio Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.
clhep numlib The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
cloudcompare geo 3D point cloud and mesh processing software
cmake devel CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
cnnpeaks bio CNN-peaks is a Convolution Neural Network(CNN) based ChIP-Seq peak calling software.
code-server tools Run VS Code on any machine anywhere and access it in the browser.
cp-analyst bio CellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CellProfiler is an image processing package to generate morphometric measurements.
cp2k chem CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
cppcheck tools Cppcheck is a static analysis tool for C/C++ code. It provides unique code analysis to detect bugs and focuses on detecting undefined behaviour and dangerous coding constructs.
cromwell tools Cromwell is a Workflow Management System geared towards scientific workflows.
crossftp tools CrossFTP is a free FTP, SFTP, WebDav, Amazon S3, Amazon Glacier, Microsoft Azure, Google storage, and OpenStack Swift client for Win, Mac, and Linux.
cuda system CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
cudnn numlib The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cufflinks bio Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
cumulus_feature_barcoding bio A fast C++ tool to extract feature-count matrix from sequence reads in FASTQ files. We uses isal-l for decompressing and Heng Li's kseq library for read parsing. It is used by Cumulus for feature-count matrix generation of cell hashing, nucleus hashing, CITE-Seq and Perturb-seq protocols, using either 10x Genomics V2 or V3 chemistry.
curl tools libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
cutadapt bio Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cytoscape bio Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
danpos bio A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2.
db_file data Perl5 access to Berkeley DB version 1.x.
dbg2olc bio A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
dbus devel D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
ddd vis DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb.
decontaminer bio decontaMiner, a tool for detecting contaminating organisms in human unmapped sequences.
deeplabcut bio DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
deeptools bio deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
diamond bio DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.
dotnet-sdk lang .NET is a free, cross-platform, open source developer platform for building many different types of applications.
double-conversion lib Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
doxygen devel Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
dragonn data The dragonn package implements Deep RegulAtory GenOmic Neural Networks (DragoNNs) for predictive modeling of regulatory genomics, nucleotide-resolution feature discovery, and simulations for systematic development and benchmarking.
drmaa tools DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.
eccodes tools ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
eigen math Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
eigensoft bio The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
elfutils lib The elfutils project provides libraries and tools for ELF files and DWARF data.
elpa math Eigenvalue SoLvers for Petaflop-Applications .
emboss bio EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
epstopdf tools Epstopdf is a Perl script that converts an EPS file to an ‘encapsulated’ PDF file (a single page file whose media box is the same as the original EPS’s bounding box).
esmf geo The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications.
evm bio The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
exonerate bio Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
expat tools Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).
fasta bio The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
fastenloc bio fastENLOC: fast enrichment estimation aided colocalization analysis enables integrative genetic association analysis of molecular QTL data and GWAS data.
fastqc bio FastQC is a Java application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report.
fastx-toolkit bio The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
ffmpeg vis A complete, cross-platform solution to record, convert and stream audio and video.
fftw numlib FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
fgwas lib fgwas is a command line tool for integrating functional genomic information into a genome-wide association study (GWAS).
fiji vis Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1
finestructure bio fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.
fltk vis FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
fmriprep bio fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI).
fontconfig vis Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
freebayes bio FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
freesurfer bio FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
freetype vis FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
freexl lib FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
fribidi lang The Free Implementation of the Unicode Bidirectional Algorithm.
fsa bio FSA:Fast Statistical Alignment, is a probabilistic multiple sequence alignment algorithm which uses a distance-based approach to aligning homologous protein, RNA or DNA sequences.
fsl bio FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
g2clib data Library contains GRIB2 encoder/decoder ('C' version).
g2lib data Library contains GRIB2 encoder/decoder and search/indexing routines.
gatk bio The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gaussian chem Gaussian is a suite of electronic-structure codes.
gawk tools The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
gcc compiler The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
gcloud-sdk tools The Cloud SDK is a set of tools for Cloud Platform. It contains gcloud, gsutil, and bq, which you can use to access Google Compute Engine, Google Cloud Storage, Google BigQuery, and other products and services from the command-line.
gd bio GD.pm - Interface to Gd Graphics Library
gdal data GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
gdb debugger The GNU Project Debugger
gdc-client tools The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.
gdk-pixbuf vis The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
gdrcopy lib A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology.
geany tools Geany is a text editor using the GTK+ toolkit with basic features of an integrated development environment.
gemma bio Genome-wide Efficient Mixed Model Association
genometools bio The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
genrich bio Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
geos math GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
gettext tools GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
gffcompare bio The program gffcompare can be used to compare, merge, annotate, and estimate accuracy of one or more GFF files (the 'query' files), when compared with a reference annotation (also provided as GFF).
ghostscript tools Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
giflib lib giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
git-lfs tools Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
glew lib The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.
glfw lib GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop. It provides a simple API for creating windows, contexts and surfaces, receiving input and events.
glib vis GLib is one of the base libraries of the GTK+ project
globus_cli tools Globus CLI is a standalone application that can be installed on the user’s machine and used to access the Globus file transfer service.
glpk tools The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
gmap-gsnap bio GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
gmp math GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gmvapich2 toolchain GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.
gnuplot vis Portable interactive, function plotting utility
go lang Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
gobject-introspection devel GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
gompi toolchain GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support.
google-api tools Google APIs give you programmatic access to Google Maps, Google Drive, YouTube, and many other Google products.
goolf toolchain GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
gperf base None
gpumd chem GPUMD stands for Graphics Processing Units Molecular Dynamics. It is a general-purpose molecular dynamics (MD) code fully implemented on graphics processing units (GPUs).
gpunufft bio GPU Regridding of arbitrary 3-D/2-D MRI data
gpustat tools dstat-like utilization monitor for NVIDIA GPUs
grace vis Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
graphene lib Graphene is a thin layer of types for graphic libraries
grass geo The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
gromacs chem GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gsl numlib The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
gst-plugins-base vis GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
gstreamer vis GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
gtk3 vis GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
gurobi math The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.
gzip tools gzip (GNU zip) is a popular data compression program as a replacement for compress
h5py data HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
harfbuzz vis HarfBuzz is an OpenType text shaping engine.
hdf data HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
hdf5 data HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
hexrd phys HEXRD provides a collection of resources for analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
hic-pro bio HiC-Pro is an optimized and flexible pipeline for Hi-C data processing.
hisat2 bio HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
homer tools HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
htslib bio A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
hunspell chem Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. Hunspell interfaces: Ispell-like terminal interface using Curses library, Ispell pipe interface, C++ class and C functions.
hwloc system The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
hypre numlib Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
icu lib ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
idl %!s(<nil>) IDL is an interpreted programming language used to create analyses and visualizations of numerical data.
igvtools bio This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
iimpi toolchain Intel C/C++ and Fortran compilers, alongside Intel MPI.
iintelmpi toolchain Intel C/C++ and Fortran compilers with IntelMPI.
imagemagick vis ImageMagick is a software suite to create, edit, compose, or convert bitmap images
imkl numlib Intel oneAPI Math Kernel Library
imkl-fftw numlib FFTW interfaces using Intel oneAPI Math Kernel Library
impi mpi Intel MPI Library, compatible with MPICH ABI
impute2 bio IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
intel toolchain Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
intel-compilers compiler Intel C, C++ & Fortran compilers (classic and oneAPI)
intelmpi mpi IntelMPI from Intel.
intltool lang The Intltool is an internationalization tool used for extracting translatable strings from source files, collecting the extracted strings with messages from traditional source files, and merging the translations into .xml, .desktop and .oaf files.
io_lib bio Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.
iqtree bio Efficient phylogenomic software by maximum likelihood
irfinder bio IRFinder is a tool for detecting intron retention from RNA-Seq experiments.
isaacgym data NVIDIA’s physics simulation environment for reinforcement learning research.
isoseqenv bio IsoDeq3 is a Scalable De Novo Isoform Discovery
itk data Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data.
jags math JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
jasper vis The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
java lang Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
jbigkit vis JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
jcuda bio Java bindings for NVIDIA CUDA and related libraries.
jdftx phys JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use.
jellyfish bio Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jemalloc lib jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
jq tools jq is a lightweight and flexible command-line JSON processor.
json-c lib JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
jtreeview vis TreeView is an open-source Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it (or parts of it) into a figure.
juicebox bio Juicer is a one-click pipeline for processing terabase scale Hi-C datasets.
julia lang Julia is a high-level, high-performance dynamic programming language for numerical computing
junit devel A programmer-oriented testing framework for Java.
jupyterlab tools Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
kallisto bio Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
kent-tools bio A set of genome utilities developed at the University of California Santa Cruz.
kim-api chem Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
knime data KNIME is an analytics platform for data mining.
kraken2 bio Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
kubectl tools The Kubernetes command-line tool, kubectl, allows you to run commands against Kubernetes clusters. You can use kubectl to deploy applications, inspect and manage cluster resources, and view logs.
lame data LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
lammps chem LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers.
lammps_flare chem Custom LAMMPS-Flare module for Paolucci group
lapack numlib LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
leda lib RStudio is a set of integrated tools designed to help you be more productive with R. LEDA is a C++ class library for efficient data types and algorithms that provide algorithmic in-depth knowledge of graph- and network problems, geometric computations, combinatorial opimization and other.
leptonica vis Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
levmar numlib Levmar is an implementation of Levenberg-Marquardt in C
lftp tools lftp is a sophisticated file transfer program supporting a number of network protocols.
lhapdf phys LHAPDF is a general purpose C++ interpolator, used for evaluating PDFs from discretised data files.
libaec lib Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
libarchive tools Multi-format archive and compression library
libdeflate system Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
libdrm lib Direct Rendering Manager runtime library.
libepoxy lib Epoxy is a library for handling OpenGL function pointer management for you
libevent lib The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
libfabric lib Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.
libffi lib The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
libgd lib GD is an open source code library for the dynamic creation of images by programmers.
libgeotiff lib Library for reading and writing coordinate system information from/to GeoTIFF files
libglu vis The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
libglvnd lib libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libgsf lib libgsf -- The G Structured File Library aims to provide an efficient extensible i/o abstraction for dealing with different structured file formats.
libgtextutils bio ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
libharu lib libHaru is a free, cross platform, open source library for generating PDF files.
libibmad system libibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.)
libibumad system libibumad is the umad kernel interface library.
libiconv lib Libiconv converts from one character encoding to another through Unicode conversion
libint chem Libint - a library for the evaluation of molecular integrals of many-body operators over Gaussian functions
libjpeg-turbo lib libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libmatheval lib GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
libpciaccess system Generic PCI access library.
libpng lib libpng is the official PNG reference library
libreadline lib The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
librmath lib The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.
librttopo lib The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores.
libspatialite lib SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
libtiff lib tiff: Library and tools for reading and writing TIFF data files
libtirpc lib Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
libtorch data A binary distribution of all headers, libraries and CMake configuration files required to depend on PyTorch.
libunwind lib The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
libxc chem Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
libxml++ lib libxml++ is a C++ wrapper for the libxml XML parser library.
libxml2 lib Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxsmm math LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
llvm compiler The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
locuszoom bio LocusZoom Standalone is for the command line (standalone) version of LocusZoom, an application for creating regional plots from genome-wide association studies built in Python and R.
longranger bio Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
lpsolve math Mixed Integer Linear Programming (MILP) solver
macs2 bio With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we presented the Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
maestro bio MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
mafft bio MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
make devel GNU version of make utility
mako devel A super-fast templating language that borrows the best ideas from the existing templating languages
mamba lang Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands.
manta bio Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
marge bio MARGE is a robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse.
mathematica %!s(<nil>)
matlab %!s(<nil>)
maven devel Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
maxquant bio MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
mayavi vis A tool for easy and interactive visualization of data.
mcr math The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
meme bio The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
mesa vis Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
meson tools Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
metamorpheus bio MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.
metis math METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
minizip lib Mini zip and unzip based on zlib
mirdeep2 bio miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).
mm-common devel The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries.
mongosh tools The MongoDB Shell, mongosh, is a fully functional JavaScript and Node.js 14.x REPL environment for interacting with MongoDB deployments. You can use the MongoDB Shell to test queries and operations directly with your database.
mothur bio Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
motif vis Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix.
mpfr math The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
mpi4py lib MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
mrtrix3 bio MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. It is developed and maintained by a team of experts in the field, fostering an active community of users from diverse backgrounds.
mrtrix3tissue bio MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software.
multiqc bio MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
mumax3 tools GPU accelerated micromagnetic simulator.
mummer bio MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
muscle bio MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.
mutect bio MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
mutsigcv bio MutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
mvapich2 mpi The MVAPICH2 software, based on MPI 3.1 standard, delivers the best performance, scalability and fault tolerance for high-end computing systems and servers using InfiniBand, Omni-Path, Ethernet/iWARP, and RoCE networking technologies.
mysqlclient lib Python interface to MySQL
namd chem NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nanopolish bio Software package for signal-level analysis of Oxford Nanopore sequencing data.
nasm lang NASM: General-purpose x86 assembler
ncbi-vdb bio The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
nccl lib The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
ncdu tools Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.
ncl data NCL is an interpreted language designed specifically for scientific data analysis and visualization.
ncurses devel The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
ncview vis Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
netcdf data NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This module bundles the C++ and Fortran libaries.
netcdf-c data NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netcdf-cxx data NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netcdf-fortran data NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netlogo math NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL.
netperf base None
neuron bio Empirically-based simulations of neurons and networks of neurons.
nextflow tools Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
ngs bio NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
ngsf bio ngsF is a program to estimate per-individual inbreeding coefficients under a probabilistic framework that takes the uncertainty of genotype's assignation into account. It avoids calling genotypes by using genotype likelihoods or posterior probabilities.
nibabies bio NiBabies is an open-source software pipeline designed to process anatomical and functional magnetic resonance imaging data. A member of the NeuroImaging PREProcessing toolS (NiPreps) family, NiBabies is designed and optimized for human infants between 0-2 years old.
ninja tools Ninja is a small build system with a focus on speed.
nlopt numlib NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
nodejs lang Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
nseg bio Nseg is used to identify low complexity sequencesi.
nspr lib Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
nss lib Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
ntl math NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.
numactl tools The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
nvhpc compiler C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
nvompi toolchain NVHPC Compiler including OpenMPI for MPI support.
nvshmem devel NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams.
ocaml compiler OCaml is an industrial-strength programming language supporting functional, imperative and object-oriented styles
ocp-models chem ocp-models is the modeling codebase for the Open Catalyst Project. It provides implementations of state-of-the-art ML algorithms for catalysis that take arbitrary chemical structures as input to predict energy / forces / positions
openbabel chem Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
openblas numlib OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
openbugs math OpenBUGS is a software application for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods.
openfoam cae OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
openjpeg lib OpenJPEG is an open-source JPEG 2000 codec written in C.
openmm chem OpenMM is a toolkit for molecular simulation using high performance GPU code.
openmpi mpi The Open MPI Project is an open source MPI-3 implementation.
openms bio OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
opensim data OpenSim is software that lets users develop models of musculoskeletal structures and create dynamic simulations of movement
openslide vis OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
openslide-python vis Python bindings for the OpenSlide libary
openspeedshop tool
optix vis OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms.
orca chem ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
p3dfft numlib P3DFFT is a library for large-scale computer simulations on parallel platforms.
p4vasp chem Variation graphs provide a succinct encoding of the sequences of many genomes.
p7zip tools p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
paintor bio PAINTOR is a statistical fine-mapping method that integrates functional genomic data with association strength from potentially multiple populations (or traits) to prioritize variants for follow-up analysis.
pango vis Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
parallel tools parallel: Build and execute shell commands in parallel
paraview vis ParaView is a scientific parallel visualizer.
parmetis numlib ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
pasapipeline bio PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
pbwt bio The pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets.
pcmsolver chem An API for the Polarizable Continuum Model.
pcre2 devel The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
peakseq bio PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
peer bio PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.
perf tools Performance analysis tools for Linux
perl lang Larry Wall's Practical Extraction and Report Language
petsc numlib PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
phonopy chem Phonopy is an open source package of phonon calculations based on the supercell approach. Phono3py calculates phonon-phonon interaction and related properties using the supercell approach.
picard bio A set of tools (in Java) for working with next generation sequencing data in the BAM format.
pigz tools pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
pipenv tools Pipenv is a tool that aims to bring the best of all packaging worlds (bundler, composer, npm, cargo, yarn, etc.) to the Python world.
pixman vis Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
pkgconf devel pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
platform-mpi mpi Platform MPI is an MPI-2 implementation from IBM.
plink bio PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
plumed chem PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
pmix lib Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability.
pnetcdf data Parallel netCDF: A Parallel I/O Library for NetCDF File Access
postgresql data PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
pov-ray vis The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
proj lib Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
proteowiz bio ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis. The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.
protobuf devel Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.
protobuf-python devel Python Protocol Buffers runtime library.
prrte lib PRRTE is the PMIx Reference RunTime Environment
psipred bio The PSIPRED Workbench provides a range of protein structure prediction methods.
pslib tools pslib is a C-library to create PostScript files on the fly. It offers many drawing primitives, inclusion of png and eps images and a very sophisticated text rendering including hyphenation, kerning and ligatures.
psmc bio PSMC infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.
pybind11 lib pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
pymol vis PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
pyspark devel PySpark is the Python API for Apache Spark. It enables you to perform real-time, large-scale data processing in a distributed environment using Python. It also provides a PySpark shell for interactively analyzing your data.
python lang Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel.
pytorch data PyTorch is a deep learning framework that puts Python first. It provides Tensors and Dynamic neural networks in Python with strong GPU acceleration.
qgis geo A Free and Open Source Geographic Information System
qt5 devel Qt is a comprehensive cross-platform C++ application framework.
qtltools bio QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
qualimap bio Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
quantumespresso chem Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
qwt lib The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
rapidsai data The RAPIDS suite of open source software libraries and APIs gives you the ability to execute end-to-end data science and analytics pipelines entirely on GPUs. Licensed under Apache 2.0, RAPIDS is incubated by NVIDIA based on extensive hardware and data science science experience. RAPIDS utilizes NVIDIA CUDA primitives for low-level compute optimization, and exposes GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces.
rasqual bio RASQUAL (Robust Allele Specific QUAntification and quality controL) maps QTLs for sequenced based cellular traits by combining population and allele-specific signals.
raxml bio RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
rclone tools Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rdp-classifier bio The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
re2c tools re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
readosm lib ReadOSM is an open source library to extract valid data from within an Open Street Map input file.
redis-cli tools Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker.
reframe devel ReFrame is a framework for writing regression tests for HPC systems.
regtools bio RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
relion bio RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
rip-md bio RIP-MD allows to apply Residue Interaction Networks (RINs) to the analysis of molecular dynamics simulations of protein.
rmats-turbo bio rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient.
rosetta bio The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rsem bio RNA-Seq by Expectation-Maximization
rstudio-server lang RStudio is an integrated development environment (IDE) for the R programming language.
ruby lang Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
rust lang Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
sagemath data SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
saint bio Significance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
saintexpress bio Significance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
salmon bio Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
sambamba bio Sambamba is a tool for processing BAM files.
samtools bio SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
sas math Statistical analysis package
sbt lang A build tool for Scala.
scalapack numlib The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
scons devel SCons is a software construction tool.
scotch math Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
sdl2 lib SDL: Simple DirectMedia Layer, a cross-platform multimedia library
seacr bio SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes (i.e. regions with no read coverage).
seqoutbias bio Molecular biology enzymes have nucleic acid preferences for their substrates; the preference of an enzyme is typically dictated by the sequence at or near the active site of the enzyme. This bias may result in spurious read count patterns when used to interpret high-resolution molecular genomics data. The seqOutBias program aims to correct this issue by scaling the aligned read counts by the ratio of genome-wide observed read counts to the expected sequence based counts for each k-mer.
sga bio SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
sgp data Gossip-based distributed optimization algorithms implemented in PyTorch
shapeit4 bio SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refactored and improved version of the SHAPEIT algorithm.
shapelib lib The Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf).
shengbte chem ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
siesta chem SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
silo data Silo is a library for reading and writing a wide variety of scientific data to binary, disk files
skopeo tools skopeo is a command line utility that performs various operations on container images and image repositories.
slatec numlib Fortran 77 numerical library.
slepc numlib SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
slicer tools 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
slim bio SLiM is an evolutionary simulation package that provides facilities for very easily and quickly constructing genetically explicit individual-based evolutionary models.
smrtlink bio PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided
snakemake tools The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
snap-stanford vis Snap.py is a Python interface for SNAP. SNAP is a general purpose, high performance system for analysis and manipulation of large networks. SNAP is written in C++ and optimized for maximum performance and compact graph representation. It easily scales to massive networks with hundreds of millions of nodes, and billions of edges.
snappy lib Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
soci lang SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++.
sortmerna bio SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
spaceranger bio A set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
spades bio SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
sparc bio Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads
spark devel Spark is Hadoop MapReduce done in memory
sparseassembler bio A sparse graph approach to de novo genome assembly
sparsehash lib An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.
spglib lib Spglib is a library for finding and handling crystal symmetries written in C.
sprng lib Scalable Parallel Pseudo Random Number Generators Library
sqlite devel SQLite: SQL Database Engine in a C Library
sratoolkit bio The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
stacks bio Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
star bio STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
stata math Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
stringtie bio StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
subversion tools Subversion is an open source version control system.
suitesparse numlib SuiteSparse is a collection of libraries manipulate sparse matrices.
sundials math SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
superlu numlib SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
superlu_mt numlib SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
swig devel SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
szip tools Szip compression software, providing lossless compression of scientific data
tbb lib Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.
tensorflow data TensorFlow is an open-source software library for Machine Intelligence.
tensorrt lib NVIDIA TensorRT is a platform for high-performance deep learning inference
tesseract vis Tesseract is an optical character recognition engine
texinfo devel Texinfo is the official documentation format of the GNU project.
texlive tools TeX Live is intended to be a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
thermorawfileparser bio Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too).
thirdorder chem A Python script to help create input files for computing anhamonic interatomic force constants, harnessing the symmetries of the system to minimize the number of required DFT calculations. A second mode of operation allows the user to build the third-order IFC matrix from the results of those runs.
tmux tools tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.
togl vis Togl is a Tk widget for OpenGL rendering
tophat bio TopHat is a fast splice junction mapper for RNA-Seq reads.
torus bio TORUS - QTL Discovery utilizing Genomic Annotations is a free software package that implements a computational procedure for discovering molecular QTLs incorporating genomic annotations.
totalview debugger TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.
tree tools Tree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty.
trf bio Tandem Repeats Finder: a program to analyze DNA sequences.
trimgalore bio Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
trimmomatic bio Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
trinity bio Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
ucc lib UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes.
ucc-cuda lib UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support.
ucx lib Unified Communication X An open-source production grade communication framework for data centric and high-performance applications
ucx-cuda lib Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support.
udunits tools UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
unrar tools RAR is a powerful archive manager.
util-linux tools Set of Linux utilities
vapor vis VAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images
varscan bio VarScan - Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vasp chem The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling.
vcell bio VCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application.
vcftools bio The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
vg bio Variation graphs provide a succinct encoding of the sequences of many genomes.
viennarna bio The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
vmd chem VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
voro++ math Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
vsearch bio VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
vtk vis The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
wannier90 chem Wannier90 is a package to calculate maximally-localised Wannier functions.
wasp bio WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.
wayland vis Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.
wdltool tools A Java command-line tool co-developed with WDL that performs utility functions, including syntax validation and generation of input JSON templates.
wigtobigwig bio The bigWig format is useful for dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
wxpython vis Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code.
wxwidgets vis wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.
x11 vis The X Window System (X11) is a windowing system for bitmap displays
x264 vis x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
x265 vis x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.
xalt lib XALT 2 is a tool to allow a site to track user executables and library usage on a cluster. When installed it can tell a site what are the top executables by Node-Hours or by the number of users or the number of times it is run. XALT 2 also tracks library usage as well. XALT 2 can also track package use by R, MATLAB or Python. It tracks both MPI and non-MPI programs.
xcrysden vis XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xerces tools Xerces-C++ is a validating XML parser written in a portable subset of C++.
xml-compile data Perl module for compilation based XML processing
xml-libxml data Perl binding for libxml2
xorg-macros devel X.org macros utilities.
xxdiff tools xxdiff is a graphical file and directories comparator and merge tool.
xxhash tools xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit.
xz tools xz: XZ utilities
yaff chem Yaff stands for 'Yet another force field'. It is a pythonic force-field code.
yambo phys YAMBO implements Many-Body Perturbation Theory (MBPT) methods (such as GW and BSE) and Time-Dependent Density Functional Theory (TDDFT), which allows for accurate prediction of fundamental properties as band gaps of semiconductors, band alignments, defect quasi-particle energies, optics and out-of-equilibrium properties of materials.
yaml-cpp tools yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec
yasm lang Yasm: Complete rewrite of the NASM assembler with BSD license
z3 tools Z3 is a theorem prover from Microsoft Research.
zlib lib zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
zstd lib Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.